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What is datelife?

datelife is an R package that allows researchers and the general audience to obtain open scientific data on the age of any organism they are interested in, by retrieving organism ages from a database of dated phylogenetic trees (aka chronograms), that have been peer-reviewed and published as part of a scientific research article, in an indexed journal (Open Tree of Life’s tree store). As such, organism ages retrieved by datelife constitute state-of-the-art, peer-reviewed, public scientific knowledge, that can be accessed and reused by experts and non-experts in the field alike.

How can you use datelife?

You can install the datelife R package on your own computer and use it locally. You can find instructions for a local installation below.

If you do not want/have time to deal with installation and R code, you can use DateLife’s interactive website application. Note that the website is not live at the moment, apologies.

Local installation of the datelife R package

datelife’s most recent stable version can be installed with:

install.packages("datelife")

datelife’s previous stable versions are available for installation from the CRAN repository. For example, to install version 0.6.1, you can run:

devtools::install_version("datelife", version="0.6.1")

You can install datelife’s development version from its GitHub repository with:

devtools::install_github("phylotastic/datelife")

Citing datelife

If you use datelife for a publication, please cite the R package and the accompanying paper:

O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright A, Schliep K, Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M, McTavish E (2024). datelife: Scientific Data on Time of Lineage Divergence for Your Taxa. R package version 0.6.9, https://doi.org/10.5281/zenodo.593938.

Sanchez-Reyes L, McTavish E, O’Meara B (2022). “datelife: Leveraging databases and analytical tools to reveal the dated Tree of Life.” bioRxiv, 782094. https://doi.org/10.1101/782094.

You can get these citations and the bibtex entry with:

citation("datelife")
toBibtex(citation("datelife"))

License

This package is free and open source software, licensed under GPL.

Acknowledgements

datelife has been developed as part of the phylotastic (NSF-funded) project, and is still under development.